Insights into the diversity and metabolic function of bacterial communities in sediments from Chilean salmon aquaculture sites

Aquaculture is an extremely valuable and rapidly expanding sector worldwide, but concerns exist related to environmental sustainability. The sediment below aquaculture farms receives inputs of antimicrobials, metal-containing products, and organic matter from uneaten food and fecal material. These inputs impact the surrounding marine microbial communities in complex ways; however, functional diversity shifts related to taxonomic composition remain poorly understood. Here, we investigated the effect of pollution from marine fish farms on sediment bacterial communities. We compared the bacterial communities and functional bacterial diversity in surface sediments at salmon aquaculture and reference sites in Chiloé, southern Chile, using Roche 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene and the predictive metagenomics approach (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt). Bacterial diversity, measured as the inverse Simpson index, was significantly lower at aquaculture than at reference sites, while species richness, based on Chao’s estimator, was not significantly different. Nevertheless, community composition differed significantly between reference and aquaculture sites. We found that Gammaproteobacteria and several taxa involved in remediating metal contamination and known to have antimicrobial resistances were enriched at aquaculture sites. However, PICRUSt predicted functions indicated a degree of functional redundancy between sites, whereas taxonomic-functional relationships indicated differences in the functional traits of specific taxa at aquaculture sites. This study provides a first step in understanding the bacterial community structure and functional changes due to Chilean salmon aquaculture and has direct implications for using bacterial shifts as indicators of aquaculture perturbations.